Sat Oct 15 10:26:23 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 10:26:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIT 137 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5716396 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.24600 40.47300 ymin,ymax (A): 28.84400 75.18000 zmin,zma (A): -10.33800 51.93900 x,y,z range (A): 55.71900 46.33600 62.27700 scale (grids/A): 0.5716396 object centre (A): 12.61350 52.01200 20.80050 number of atom coordinates read : 2681 total number of charged atoms : 2530 net assigned charge : -4.985987 assigned positive charge : 396.8353 centred at (gu) : 90.20341 91.23473 90.26926 assigned negative charge : -401.8222 centred at (gu) : 90.23033 91.22604 90.26290 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5720 nv = 96 ne = 84 npr = 53850 no. pairs analyzed = 53850 no. exposed pairs = 3496 no. arc points = 24833 no. surface atoms = 1182 nbur = 1499 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 252 mr = 2916 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2401 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5211638E-10 -7.6154699E-10 midg,1,midg; midg,igrid,midg -7.0925144E-10 -9.0379881E-10 1,midg,midg; igrid,midg,midg -3.9092166E-10 -1.2759558E-09 gauss-seidel spectral radius is 0.9841883 estimated iterations to convergence 65 setup time was (sec) 0.6000000 now iterating at: 10:26:24 rms-change max change #iterations 8.9466333E-02 15.47854 at 10iterations 6.6006579E-03 1.069612 at 20iterations 4.8687868E-04 7.5998306E-02 at 30iterations 3.7723039E-05 6.2813759E-03 at 40iterations 3.0865781E-06 4.6157837E-04 at 50iterations finished qdiffx linear iterations at : 10:26:31 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 3.0865781E-06 4.6157837E-04 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 10:26:32 4.148u 0.412s 0:08.54 53.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 10:26:32 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIT 137 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.714919 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.24600 40.47300 ymin,ymax (A): 28.84400 75.18000 zmin,zma (A): -10.33800 51.93900 x,y,z range (A): 55.71900 46.33600 62.27700 scale (grids/A): 1.714919 object centre (A): 12.61350 52.01200 20.80050 number of atom coordinates read : 2681 total number of charged atoms : 2530 net assigned charge : -4.985987 assigned positive charge : 396.8353 centred at (gu) : 90.60938 93.70365 90.80689 assigned negative charge : -401.8222 centred at (gu) : 90.69091 93.67780 90.78848 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24833 grid for indexing accessible points = 1.400000 m= 19702 mr = 41724 m= 2337 mr = 13703 m= 71 mr = 1251 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 28221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19565 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5716396 object centre at (A) : 12.61350 52.01200 20.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2599045E-03 -3.2844104E-02 midg,1,midg; midg,igrid,midg 9.4321626E-04 -4.9264291E-03 1,midg,midg; igrid,midg,midg -9.7828591E-03 -5.8786324E-03 gauss-seidel spectral radius is 0.9983289 estimated iterations to convergence 194 setup time was (sec) 0.7800000 now iterating at: 10:26:34 rms-change max change #iterations 3.494394 177.2938 at 10iterations 1.503346 70.36342 at 20iterations 0.6480152 22.41220 at 30iterations 0.2796213 10.93447 at 40iterations 0.1209048 4.581695 at 50iterations 5.2029300E-02 2.182695 at 60iterations 2.2497645E-02 0.8079586 at 70iterations 9.6815573E-03 0.4091415 at 80iterations 4.2066472E-03 0.1518478 at 90iterations 1.8118861E-03 6.9335938E-02 at 100iterations 7.8545668E-04 2.5445223E-02 at 110iterations 3.3769297E-04 1.1203766E-02 at 120iterations finished qdiffx linear iterations at : 10:26:51 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 3.3769297E-04 1.1203766E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 10:26:51 9.287u 0.502s 0:19.55 50.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 10:26:51 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIT 137 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.572378 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.24600 40.47300 ymin,ymax (A): 28.84400 75.18000 zmin,zma (A): -10.33800 51.93900 x,y,z range (A): 55.71900 46.33600 62.27700 scale (grids/A): 2.572378 object centre (A): 12.61350 52.01200 20.80050 number of atom coordinates read : 2681 total number of charged atoms : 2530 net assigned charge : -4.985987 assigned positive charge : 396.8353 centred at (gu) : 90.91385 95.55519 91.21020 assigned negative charge : -401.8222 centred at (gu) : 91.03629 95.51659 91.18270 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 145936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24833 grid for indexing accessible points = 1.400000 m= 66698 mr = 102390 m= 20380 mr = 52693 m= 3690 mr = 15571 m= 331 mr = 2477 m= 8 mr = 165 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 63745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20231 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.714919 object centre at (A) : 12.61350 52.01200 20.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3133703E-02 -0.4268521 midg,1,midg; midg,igrid,midg 2.4911497E-02 -9.7080834E-02 1,midg,midg; igrid,midg,midg -0.1153148 -3.9905038E-02 gauss-seidel spectral radius is 0.9991765 estimated iterations to convergence 275 setup time was (sec) 1.610000 now iterating at: 10:26:57 rms-change max change #iterations 8.856130 355.9784 at 10iterations 5.023905 140.9548 at 20iterations 2.833758 65.91392 at 30iterations 1.598792 37.53305 at 40iterations 0.8948819 21.77576 at 50iterations 0.5022312 10.85670 at 60iterations 0.2804718 6.374998 at 70iterations 0.1562821 3.621264 at 80iterations 8.7171547E-02 1.890135 at 90iterations 4.8697386E-02 1.078907 at 100iterations 2.7118104E-02 0.5675983 at 110iterations 1.5074759E-02 0.3691940 at 120iterations 8.4247366E-03 0.1847281 at 130iterations 4.6844003E-03 9.4631195E-02 at 140iterations 2.6062140E-03 5.4000378E-02 at 150iterations 1.4502621E-03 3.4790218E-02 at 160iterations 8.0907549E-04 1.7959595E-02 at 170iterations 4.4938616E-04 9.4776154E-03 at 180iterations finished qdiffx linear iterations at : 10:27:30 total time elapsed so far: 21.74000 # loops : 180 mean,max change (kT/e) : 4.4938616E-04 9.4776154E-03 energy calculations done at 21.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.90000 DelPhi exited at 10:27:31 21.904u 0.607s 0:39.38 57.1% 0+0k 0+0io 0pf+0w